Protein synthesis

The genetic code

A sequence of three bases codes for one amino acid. In DNA that sequence is a triplet; in mRNA it is a codon; the matching sequence on tRNA is an anticodon.

Three properties of the code are examinable in their own right:

• It is a triplet code. Three bases per amino acid. Two would give only 16 combinations, which is not enough for 20 amino acids. Three gives 64.
• It is degenerate. Most amino acids have more than one codon, because there are 64 codons and only 20 amino acids. This is why some substitution mutations have no effect.
• It is universal. Almost every organism uses the same code, which is what makes genetic engineering possible: a human gene put into a bacterium is read the same way.
• It is non-overlapping. Each base belongs to one triplet only, read consecutively from a fixed start point. This is why a deletion causes a frameshift.

Three codons are stop codons, signalling the end of a polypeptide. AUG codes for methionine and also acts as the start codon.

The two strands

Only one of the two DNA strands is copied. Getting the names right matters:

• The template strand, also called the transcribed or antisense strand, is the one read by RNA polymerase. The mRNA is complementary to it.
• The coding strand, also called the non-transcribed or sense strand, is the other one. The mRNA has the same sequence as it, except that uracil replaces thymine.

Worked example

A template strand reads TAC GGA CTT.

The mRNA is complementary to it, with U in place of T:

AUG CCU GAA

The anticodons on the tRNA molecules are complementary to the mRNA codons:

UAC GGA CUU

Notice that the anticodons match the original template sequence, with U for T. That is a useful check on your working.

The coding strand would read ATG CCT GAA, the same as the mRNA with T for U.

Transcription

Making mRNA from a DNA template. It happens in the nucleus.

1. DNA helicase, or the polymerase itself, breaks the hydrogen bonds and unwinds a section of the double helix, exposing the bases of the gene.
2. Free RNA nucleotides pair with the exposed bases of the template strand, A with U, T with A, C with G.
3. RNA polymerase joins the RNA nucleotides together by phosphodiester bonds, moving along the template strand.
4. The completed mRNA detaches, the DNA rewinds, and the mRNA leaves the nucleus through a nuclear pore.

Only the gene being expressed is transcribed, not the whole chromosome, and different genes are transcribed in different cells. That is what makes a liver cell different from a nerve cell despite identical DNA.

Translation

Building the polypeptide from the mRNA. It happens at a ribosome, in the cytoplasm or on the rough endoplasmic reticulum.

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1. The mRNA attaches to a ribosome. The ribosome holds two codons at a time.
2. A tRNA molecule with an anticodon complementary to the first codon arrives, carrying its specific amino acid. Hydrogen bonds form between codon and anticodon.
3. A second tRNA binds to the next codon.
4. A peptide bond forms between the two amino acids, catalysed by the ribosome.
5. The ribosome moves along one codon. The first tRNA leaves, free to collect another amino acid of the same kind.
6. The cycle repeats until a stop codon is reached, at which point the polypeptide is released.

Several ribosomes often work along the same mRNA at once, forming a polysome, so many copies of the protein are made from one transcript.

The new polypeptide then folds into its tertiary structure. If it is destined for secretion, it passes through the rough endoplasmic reticulum and the Golgi body and leaves by exocytosis, which is the route described in topic 3.1.

The three RNAs

Each tRNA is specific: the anticodon and the amino acid binding site correspond, so a tRNA with anticodon UAC always carries methionine.

Where the two stages happen, and why it matters

Transcription is in the nucleus and translation is in the cytoplasm, because DNA cannot leave the nucleus. mRNA is the messenger precisely because it is small enough to pass through a nuclear pore and the chromosome is not.

In prokaryotes there is no nucleus, so transcription and translation happen in the same place and can happen at the same time on the same molecule.

How a mutation reaches the protein

The chain runs: DNA base sequence → mRNA codon sequence → amino acid sequence → tertiary structure → function.

A change at the first link travels along it.

• A substitution in a degenerate position changes the codon but not the amino acid, so the protein is unchanged. This is a silent mutation.
• A substitution that changes the amino acid puts a different R group into the chain. If it is in or near the active site of an enzyme, or at a point where an important bond forms, the tertiary structure changes and function is lost. If it is elsewhere, the effect may be small.
• A substitution producing a stop codon truncates the protein, usually destroying it.
• A deletion or insertion shifts the reading frame, so every codon downstream is misread and the protein is almost always non-functional.

Common mistakes

• Saying mRNA is complementary to the coding strand. It is complementary to the template strand and identical to the coding strand.
• Saying the anticodon is on the mRNA. The codon is on mRNA; the anticodon is on tRNA.
• Saying transcription happens at the ribosome. Transcription is in the nucleus; translation is at the ribosome.
• Saying tRNA "makes" the amino acid. It carries one that already exists in the cytoplasm.
• Saying the code is degenerate "because some codons are unused". Degeneracy means several codons code for the same amino acid.

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